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annotate unzip.xml @ 2:57f0914ddb7b draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
author imgteam
date Fri, 14 Apr 2023 19:02:41 +0000
parents 38eec75fbe9b
children
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2
57f0914ddb7b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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1 <tool id="unzip" name="Unzip" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Unzip a file</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">6.0</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 <token name="@PROFILE@">22.01</token>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">unzip</requirement>
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10 <requirement type="package" version="1.34">tar</requirement>
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11 </requirements>
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12 <command>
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13 <![CDATA[
0
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14 mkdir ./out &&
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
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15 #if $input_file.is_of_type("zip"):
2
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16 unzip
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17 #if $extract_options['extract_all'] == 'False'
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18 -p '$input_file' '$extract_options["pathtofile"]' > out.data
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19 #else
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20 '$input_file' -d out/
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21 #end if
0
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22 #end if
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23 #if $input_file.is_of_type("tar"):
2
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24 tar
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25 #if $extract_options['extract_all'] == 'False'
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26 xfO '$input_file' '$extract_options["pathtofile"]' > out.data
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27 #else
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28 -xf '$input_file' -C ./out/
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29 #end if
0
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30 #end if
2
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31 &&
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32
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33 ## Flatten any potential directory structure, e.g.
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34 ## out/sub1/subsub2/fileA.ext -> out/sub1_subsub2_fileA.ext
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35 find out -type f | cut -d '/' -f 2- | grep '/' | xargs -I % sh -c "mv out/% out/\\$(echo % | tr / _)"
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36 ]]>
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37 </command>
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38 <inputs>
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39 <param label="input_file" name="input_file" type="data" format="zip,tar"/>
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40 <conditional name="extract_options">
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41 <param label="Extract single file" name="extract_all" type="select">
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42 <option selected="True" value="True">All files</option>
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43 <option value="False">Single file</option>
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44 </param>
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45 <when value="True"></when>
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46 <when value="False">
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47 <param name="pathtofile" type="text" value="" label="Filepath">
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48 <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
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49 <validator type="expression" message="No comma (,) allowed">',' not in value</validator>
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50 <validator type="expression" message="No asterisk (*) allowed">'*' not in value</validator>
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51 <validator type="expression" message="No leading slash (/) allowed">str(value)[0] != '/'</validator>
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52 </param>
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53 </when>
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54 </conditional>
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55 </inputs>
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56 <outputs>
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57 <data auto_format="true" name="unzipped_single" from_work_dir="out.data" label="${tool.name} on ${on_string}">
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58 <filter>extract_options['extract_all'] == 'False'</filter>
0
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59 </data>
2
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60 <collection name="unzipped" type="list" label="${tool.name} on ${on_string} all files as collection">
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61 <discover_datasets directory="out" pattern="(?P&lt;designation&gt;.+?)(\.(?P&lt;ext&gt;[^\._]+))?$" visible="false" format="auto"/>
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62 <!-- pattern=__designation_and_ext__ = (?P&lt;designation&gt;.*)\.(?P&lt;ext&gt;[^\._]+)? would discard files without extensions -->
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63 <filter>extract_options['extract_all'] == 'True'</filter>
0
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64 </collection>
2
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65 </outputs>
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66 <tests>
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67 <test expect_num_outputs="1">
0
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68 <param name="input_file" value="input.zip" ftype="zip"/>
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69 <param name="extract_all" value="False"/>
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70 <param name="pathtofile" value="input.png"/>
2
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71 <output name="unzipped_single" file="input.png" ftype="png" compare="sim_size"/>
0
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72 </test>
2
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73 <test expect_num_outputs="1">
0
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74 <param name="input_file" value="input.zip" ftype="zip"/>
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75 <param name="extract_all" value="True"/>
2
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76 <output_collection name="unzipped" type="list" count="2">
1
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77 <element name="input" file="input.png" ftype="png" compare="sim_size"/>
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78 <element name="res" file="res.tiff" ftype="tiff" compare="sim_size"/>
0
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79 </output_collection>
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80 </test>
2
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81 <!-- Binary files without file extension -->
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82 <test expect_num_outputs="1">
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83 <param name="input_file" value="input_binary.zip" ftype="zip"/>
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84 <param name="extract_all" value="True"/>
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85 <output_collection name="unzipped" type="list" count="2">
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86 <element name="yelp" file="yelp" compare="sim_size"/>
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87 <element name="yes" file="yes" compare="sim_size"/>
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88 </output_collection>
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89 </test>
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90 <!-- Compressed object with subfolders, each containing files -->
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91 <test expect_num_outputs="1">
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92 <param name="input_file" value="subfolders.zip" ftype="zip"/>
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93 <param name="extract_all" value="True"/>
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94 <output_collection name="unzipped" type="list" count="4">
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95 <element name="binaries_yelp" file="yelp" compare="sim_size"/>
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96 <element name="binaries_yes" file="yes" compare="sim_size"/>
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97 <element name="images_input" file="input.png" ftype="png" compare="sim_size"/>
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98 <element name="images_res" file="res.tiff" ftype="tiff" compare="sim_size"/>
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99 </output_collection>
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100 </test>
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101 <test expect_num_outputs="1">
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102 <param name="input_file" value="input.tar" ftype="tar"/>
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103 <param name="extract_all" value="False"/>
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104 <param name="pathtofile" value="input.png"/>
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105 <output name="unzipped_single" file="input.png" ftype="png" compare="sim_size"/>
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106 </test>
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107 <test expect_num_outputs="1">
0
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108 <param name="input_file" value="input.tar" ftype="tar"/>
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109 <param name="extract_all" value="True"/>
2
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110 <output_collection name="unzipped" type="list" count="2">
1
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111 <element name="input" file="input.png" ftype="png" compare="sim_size"/>
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112 <element name="res" file="res.tiff" ftype="tiff" compare="sim_size"/>
0
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113 </output_collection>
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114 </test>
2
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115 </tests>
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116 <help>
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117 **What it does**
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118
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119 Unzip a folder containing file(s) of various types. If multiple files are asked to be retained, the output will be a collection containing all files within the zip or tar archive.
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120 </help>
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121 <citations>
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122 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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123 </citations>
0
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124 </tool>
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125